X-group (possible homology)

4045 barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes

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Ligands and drugs

647

Member domains

384

with ligand contacts (≤ 4 Å)

59.4% of members

368

with DrugDomain annotations

56.9% of members

329

with a DrugBank compound

50.9% of members

Aggregated over all current member domains of this group. Drug annotations come from DrugDomain; buffers and crystallization additives are excluded from the tables below.

Chemical profile

ClassyFire chemical superclasses of the ligands bound by this X-group's proteins, from DrugDomain annotations.

Proteins with classified ligands

Superclasses bound (of 23)

7.5

Superclasses per 20 proteins

narrower than 53% of the 256 X-groups with enough proteins to compare (median 7.6)

The raw number of superclasses rises with the number of proteins sampled; the per-20 value compares X-groups at equal depth.

Superclass	Proteins	Expected	Ratio	Significance
Organoheterocyclic compounds	36	6.4	5.65×	q < 0.0001
Organic acids and derivatives	10	6.4	1.56×	q = 0.18
Homogeneous non-metal compounds	13	8.9	1.46×	q = 0.18
Homogeneous metal compounds	5	20.3	0.25×	q < 0.0001
Organic oxygen compounds	2	8.3	0.24×	q = 0.02
Nucleosides, nucleotides, and analogues	0	11.5	0	q < 0.0001
Benzenoids	4	3.0	1.32×	not tested
Phenylpropanoids and polyketides	1	0.9	1.16×	not tested
Organic nitrogen compounds	1	1.3	0.76×	not tested
Lipids and lipid-like molecules	3	4.6	0.65×	not tested

enriched (q < 0.05)depleted (q < 0.05)not significantnot tested (expected < 5)

Unit: a protein (UniProt accession) with a ligand-binding domain in this X-group, counted once per superclass. Expected counts use each superclass's frequency across all ligand-binding X-groups; significance is Fisher's exact test with Benjamini–Hochberg correction. Buffers and crystallization additives are excluded. ECOD v295.2; the method follows the ECOD 2027 update, whose published figures used a slightly different artifact filter.

DrugBank compounds

DrugBank	PDB ligand	Name	Domains
DB00114	PLP	Pyridoxal phosphate	245
DB02142	PMP	Pyridoxamine-5'-Phosphate	22
DB04237	TAM	Tris(Hydroxyethyl)Aminomethane	12
DB00996	GBN	Gabapentin	9
DB03993	4MV	Isocaproic acid	8
DB01813	PPE	Pyridoxyl-Glutamic Acid-5'-Monophosphate	6
DB03229	COI	alpha-Ketoisocaproic acid	5
DB08845	AKG	Oxogluric acid	5
DB00142	GLU	Glutamic acid	4
DB00160	ALA	Alanine	4
DB07544	CBC	N'-(5-CHLOROBENZOFURAN-2-CARBONYL)-2-(TRIFLUOROMETHYL)BENZENESULFONOHYDRAZIDE	4
DB02038	DCS	D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide	3
DB02054	GAB	Gabaculine	3
DB03553	GUA	Glutaric Acid	3
DB03662	PY5	Vitamin B6 Complexed with 2-Amino-Pentanoic Acid	3
DB04063	2ML	alpha-Methylleucine	3
DB00149	—	Leucine	2
DB00167	—	Isoleucine	2
DB01993	PDD	N-(5'-Phosphopyridoxyl)-D-Alanine	2
DB02024	HCI	3-phenylpropionic acid	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
PLP	PYRIDOXAL-5'-PHOSPHATE	251
CL	CHLORIDE ION	66
PMP	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE	25
9HC	[4-[3-(4-bromophenyl)-3-oxidanylidene-propyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl phosphate	12
TAM	TRIS(HYDROXYETHYL)AMINOMETHANE	12
GBN	[1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID	9
4MV	4-METHYL VALERIC ACID	8
IOD	IODIDE ION	8
PXG	3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID	8
OCF	3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid	7
NAmetal	SODIUM ION	6
PPE	4-[(1,3-DICARBOXY-PROPYLAMINO)-METHYL]-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM	6
AKG	2-OXOGLUTARIC ACID	5
COI	2-OXO-4-METHYLPENTANOIC ACID	5
ALA	ALANINE	4
CBC	N'-(5-CHLOROBENZOFURAN-2-CARBONYL)-2-(TRIFLUOROMETHYL)BENZENESULFONOHYDRAZIDE	4
UNL	Unknown ligand	4
UTK	4-[2,4-bis(oxidanylidene)-6-(trifluoromethyl)-1H-pyrimidin-3-yl]-5-fluoranyl-2-(2-methylphenoxy)benzenecarbonitrile	4
UTQ	3-(5-chloranyl-2,4-dimethoxy-phenyl)-6-(trifluoromethyl)-1H-pyrimidine-2,4-dione	4
2ML	2-METHYLLEUCINE	3